First pherogram displaying example added to the alignment editor. (Path to test resou...

diff --git a/.gitattributes b/.gitattributes
index b75d7ac6ee138e7f99701d499baaa4c1dadfcd78..ba97fa66eb6ab405e73256b461c339d30fb6dda9 100644 (file)
--- a/.gitattributes
+++ b/.gitattributes
@@ -588,6 +588,7 @@ eu.etaxonomy.taxeditor.editor/src/main/java/eu/etaxonomy/taxeditor/editor/view/u
 eu.etaxonomy.taxeditor.editor/src/main/java/eu/etaxonomy/taxeditor/editor/view/uses/operation/CreateUseRecordOperation.java -text
 eu.etaxonomy.taxeditor.editor/src/main/java/eu/etaxonomy/taxeditor/editor/view/uses/operation/CreateUseSummaryOperation.java -text
 eu.etaxonomy.taxeditor.editor/src/main/resources/TaonDescriptionEditor.screen -text
+eu.etaxonomy.taxeditor.editor/src/main/resources/TestPherogram_qualityScore.scf -text
 eu.etaxonomy.taxeditor.editor/src/main/resources/log4j.properties -text
 eu.etaxonomy.taxeditor.editor/src/test/java/eu/etaxonomy/taxeditor/editor/Application.java -text
 eu.etaxonomy.taxeditor.editor/src/test/java/eu/etaxonomy/taxeditor/editor/ApplicationActionBarAdvisor.java -text

diff --git a/eu.etaxonomy.taxeditor.editor/src/main/java/eu/etaxonomy/taxeditor/editor/molecular/AlignmentEditor.java b/eu.etaxonomy.taxeditor.editor/src/main/java/eu/etaxonomy/taxeditor/editor/molecular/AlignmentEditor.java
index 089eca7f1620b1aca35df6613fb73acaf112c009..fbc5c0cd5d5c1c47c2809b72a765b86bea043d79 100644 (file)
--- a/eu.etaxonomy.taxeditor.editor/src/main/java/eu/etaxonomy/taxeditor/editor/molecular/AlignmentEditor.java
+++ b/eu.etaxonomy.taxeditor.editor/src/main/java/eu/etaxonomy/taxeditor/editor/molecular/AlignmentEditor.java
@@ -10,17 +10,23 @@
 package eu.etaxonomy.taxeditor.editor.molecular;
 
 
+import java.io.File;
+
 import info.bioinfweb.commons.bio.biojava3.alignment.SimpleAlignment;
 import info.bioinfweb.commons.bio.biojava3.alignment.template.Alignment;
 import info.bioinfweb.commons.bio.biojava3.core.sequence.compound.AlignmentAmbiguityNucleotideCompoundSet;
 import info.bioinfweb.libralign.AlignmentArea;
 import info.bioinfweb.libralign.dataarea.implementations.ConsensusSequenceArea;
 import info.bioinfweb.libralign.dataarea.implementations.SequenceIndexArea;
+import info.bioinfweb.libralign.dataarea.implementations.pherogram.PherogramArea;
+import info.bioinfweb.libralign.pherogram.BioJavaPherogramProvider;
 import info.bioinfweb.libralign.sequenceprovider.implementations.BioJavaSequenceDataProvider;
 import info.bioinfweb.libralign.sequenceprovider.tokenset.BioJavaTokenSet;
 
+import org.biojava.bio.chromatogram.ChromatogramFactory;
 import org.biojava3.core.sequence.DNASequence;
 import org.biojava3.core.sequence.compound.NucleotideCompound;
+import org.eclipse.core.resources.ResourcesPlugin;
 import org.eclipse.core.runtime.IProgressMonitor;
 import org.eclipse.swt.SWT;
 import org.eclipse.swt.widgets.Composite;
@@ -48,26 +54,75 @@ public class AlignmentEditor extends EditorPart {
 
 
        private AlignmentArea createAlignmentArea() {
-               Alignment<DNASequence, NucleotideCompound> alignment = 
-                               new SimpleAlignment<DNASequence, NucleotideCompound>();
-               alignment.add("Sequence 1", new DNASequence("ATCGTAGATCGTAGATCGTAGATCGTAGATCGTAGATCGTAGATCGTAG"));
-               alignment.add("Sequence 2", new DNASequence("AT-GTTG"));
-               alignment.add("Sequence 3", new DNASequence("AT-GTAG"));
-               
-               BioJavaSequenceDataProvider<DNASequence, NucleotideCompound> sequenceProvider = 
-                               new BioJavaSequenceDataProvider<DNASequence, NucleotideCompound>(
-                                               new BioJavaTokenSet<NucleotideCompound>(
-                                                               AlignmentAmbiguityNucleotideCompoundSet.getAlignmentAmbiguityNucleotideCompoundSet()),
-                                               alignment);
+               try {
+                       //ResourcesPlugin.getWorkspace().getRoot().getFile("/eu.etaxonomy.taxeditor.editor/src/main/resources/TestPherogram_qualityScore.scf");
+                       //System.out.println(AlignmentEditor.class.getResource("/"));
+                       //System.out.println(AlignmentEditor.class.getResource("/../resources/TestPherogram_qualityScore.scf"));
+                       BioJavaPherogramProvider pherogramProvider = new BioJavaPherogramProvider(ChromatogramFactory.create(
+                                       new File("D:\\Users\\BenStoever\\Documents\\Studium\\Projekte\\Promotion\\EDITor\\Quelltexte\\LibrAlign branch\\Repository\\eu.etaxonomy.taxeditor.editor\\src\\main\\resources\\TestPherogram_qualityScore.scf")));
+                   //TODO Replace this absolute path with a path working with every workspace location.
+                       
+                       Alignment<DNASequence, NucleotideCompound> alignment = 
+                                       new SimpleAlignment<DNASequence, NucleotideCompound>();
+                       alignment.add("Sequence 1", new DNASequence("ATCGTAGATCGTAGATCGTAGATCGTAGATCGTAGATCGTAGATCGTAG"));
+                       alignment.add("Sequence 2", new DNASequence("AT-GTTG"));
+                       alignment.add("Sequence 3", new DNASequence("AT-GTAG"));
+                       
+                       StringBuffer seqBuffer = new StringBuffer(pherogramProvider.getSequenceLength());
+                       for (int i = 1; i <= pherogramProvider.getSequenceLength(); i++) {
+                               seqBuffer.append(pherogramProvider.getBaseCall(i).getUpperedBase());
+                       }
+                       alignment.add("Sequence 4", new DNASequence("-----" + seqBuffer.substring(0, 38) + 
+                                       seqBuffer.substring(39, 49) + "--" + seqBuffer.substring(49)));  // One A is deleted for shift change specified below. 
+                       
+                       BioJavaSequenceDataProvider<DNASequence, NucleotideCompound> sequenceProvider = 
+                                       new BioJavaSequenceDataProvider<DNASequence, NucleotideCompound>(
+                                                       new BioJavaTokenSet<NucleotideCompound>(
+                                                                       AlignmentAmbiguityNucleotideCompoundSet.getAlignmentAmbiguityNucleotideCompoundSet()),
+                                                       alignment);
+                       
+                       AlignmentArea result = new AlignmentArea();
+                       result.setSequenceProvider(sequenceProvider, false);
+                       SequenceIndexArea sequenceIndexArea = new SequenceIndexArea(result);
+                       //sequenceIndexArea.setFirstIndex(5);
+                       //sequenceIndexArea.setHeight(25);
+                       result.getDataAreas().getTopAreas().add(sequenceIndexArea);
+                       
+                       PherogramArea pherogramArea = new PherogramArea(result, pherogramProvider);
+                       pherogramArea.setFirstSeqPos(34 + 5);
+                       pherogramArea.setLeftCutPosition(34);
+                       pherogramArea.setRightCutPosition(820);
+                       pherogramArea.getAlignmentModel().setShiftChange(38, -1);
+                       pherogramArea.getAlignmentModel().setShiftChange(49, 2);
+                       result.getDataAreas().getSequenceAreas(sequenceProvider.sequenceIDByName("Sequence 4")).add(pherogramArea);
+                       
+                       result.getDataAreas().getBottomAreas().add(new ConsensusSequenceArea(result));
+                       return result;
+               }
+               catch (Exception e) {
+                       throw new RuntimeException(e);
+               }
                
-               AlignmentArea result = new AlignmentArea();
-               result.setSequenceProvider(sequenceProvider, false);
-               SequenceIndexArea sequenceIndexArea = new SequenceIndexArea(result);
-               //sequenceIndexArea.setFirstIndex(5);
-               //sequenceIndexArea.setHeight(25);
-               result.getDataAreas().getTopAreas().add(sequenceIndexArea);
-               result.getDataAreas().getBottomAreas().add(new ConsensusSequenceArea(result));
-               return result;
+//             Alignment<DNASequence, NucleotideCompound> alignment = 
+//                             new SimpleAlignment<DNASequence, NucleotideCompound>();
+//             alignment.add("Sequence 1", new DNASequence("ATCGTAGATCGTAGATCGTAGATCGTAGATCGTAGATCGTAGATCGTAG"));
+//             alignment.add("Sequence 2", new DNASequence("AT-GTTG"));
+//             alignment.add("Sequence 3", new DNASequence("AT-GTAG"));
+//             
+//             BioJavaSequenceDataProvider<DNASequence, NucleotideCompound> sequenceProvider = 
+//                             new BioJavaSequenceDataProvider<DNASequence, NucleotideCompound>(
+//                                             new BioJavaTokenSet<NucleotideCompound>(
+//                                                             AlignmentAmbiguityNucleotideCompoundSet.getAlignmentAmbiguityNucleotideCompoundSet()),
+//                                             alignment);
+//             
+//             AlignmentArea result = new AlignmentArea();
+//             result.setSequenceProvider(sequenceProvider, false);
+//             SequenceIndexArea sequenceIndexArea = new SequenceIndexArea(result);
+//             //sequenceIndexArea.setFirstIndex(5);
+//             //sequenceIndexArea.setHeight(25);
+//             result.getDataAreas().getTopAreas().add(sequenceIndexArea);
+//             result.getDataAreas().getBottomAreas().add(new ConsensusSequenceArea(result));
+//             return result;
        }
        
        

diff --git a/eu.etaxonomy.taxeditor.editor/src/main/resources/TestPherogram_qualityScore.scf b/eu.etaxonomy.taxeditor.editor/src/main/resources/TestPherogram_qualityScore.scf
new file mode 100644 (file)
index 0000000..e680999
Binary files /dev/null and b/eu.etaxonomy.taxeditor.editor/src/main/resources/TestPherogram_qualityScore.scf differ